New “Link” functionality allows the user to specify when a lung RNA result is related to results from a GeneRead QIAact Lung DNA Panel analysis workflow. When QCI Analyze results are linked, selected actions are performed for both sample analyses simultaneously. Specifically, when using the built-in upload to QCI Interpret, the results are merged and an all-in-one QCI Interpret report is obtained.

For QCI Analyze set up with GeneRead Link, it is now possible to manually import FASTQ files into QCI Analyze, and start an analysis workflow on the data. The results will be local to QCI Analyze, and thus not sent to GeneRead Link.

New options for custom configuration of analysis workflows allow the user to set a lower frequency threshold for variants that will be included in the QCI Analyze report variant table 2, “Available for review”. The frequency threshold for variants initially listed in variant table 1, “Reported variants”, will remain fixed.

Comparison reports can now be deleted.

Improvements:

A new layout of the user interface is introduced:

The functionalities in the “Start” and “Status” tabs have been merged into the “Analyses” page.

Sample analyses are now presented in a paged tabular view, as opposed to being distributed in tiles according to their status. This enables users to work with thousands of sample analyses in the system.

Improved performance when working with thousands of sample analyses in the system.

Minor updates to the Variant of Interest (VOI) list for the ATP and Lung DNA analysis workflows ensure that all alternate codon changes giving rise to a specific amino acid variant of interest is now annotated as VOI in the variant tables. This does not impact variant calling and filtering, only the VOI annotation.

The QCI Interpret upload dialog now contains the field Pertinent Negative Gene(s)

Updates:

As a consequence of introducing new options for custom configuration of analysis workflows, the order of variant filtering in the analysis workflows was changed. This will potentially remove a variant from the report that before just barely passed the filter criteria, and similarly, report a variant that before would not have passed the filter criteria.

A Samples Overview graph is no longer available. When filtering the list of sample analyses with respect to an analysis status, the number of sample analyses with the specified status is displayed.

Result status is no longer indicated as a red/yellow/green indicator in the overview, as it could be mistaken as an indication of QC issues for the sample analysis. The result status information is still accessible from the analysis overview, by selecting a sample analysis.

The previous and next buttons have been removed from the Track Viewer. Instead, users can navigate between variants via the variant tables.

The QCI Interpret upload dialog field “Promotion Code” has been removed as it has become obsolete.

Bug fixes:

Fixed issues related to the Track Viewer functionality:

It is now possible to refresh (F5) the browser while the Track Viewer is visible without breaking the Track Viewer visualization.

Sometimes, the “Mapped reads” track would not be displayed when selecting a variant in section 3.

Now, only genes from the chromosome currently shown are displayed in the “Jump to gene” drop down list.

Sometimes, the “Mapped reads” track height did not update correctly when zooming out.

Fixed issues related to other functionality:

The "Save as PDF" and "Save as VCF" actions no longer cache the output, thus every time a PDF or VCF is requested a new file is created instead to ensure that potential changes to the report are represented in the PDF and VCF.

The sample counter of a flow cell plan in the GeneReader Planner now always show the correct number of samples on the flow cell plan.

The analysis configuration tile is now updated properly after a Genomics Server restart.

The variant tables of the HTML report have been improved to render properly after filtering.

Known issues:

The variant annotation “Qual”, given in the tables in section 3 of the review report, displays a “0”, when it is actually Not-a-Number (NaN), and the cell should be empty instead. The tooltip in the track viewer does indicate that the “Qual” value is NaN. Users are encouraged, if in doubt, to inspect the tooltip before filtering out the variant manually which could potentially lead to false negative variants.GeneRead Databank 1.1.0

New application:

Automatically moves GR 1.1 data from the GR workstation to the QCI Powerstation for mid-term storage

Automatically moves GR 1.1 data to a long-term archive, which can be a Network Attached Storage (NAS) device or a Microsoft Azure BLOB Storage

Allows to search and access the stored data using the web browsers Microsoft Internet Explorer, Firefox or Google Chrome

Faster transfer of result reports to GeneRead Link. GeneRead QIAcube checks the presence of reports to be uploaded to GeneRead Link periodically. The interval is now reduced from 5 minutes to 1 minute in order to immediately notify the user on the completion of the GeneRead QIAcube run.

Improving the error message when report is getting uploaded multiple times. Upload error message has been modified to give more information to the user to check the status of the report before trying to upload again

User notification when run set up is performed manually on GeneRead QIAcube while GeneRead QIAcube is connected to GeneRead Link. A message is displayed to the user when the user enters library pools manually on GeneRead QIAcube. The user is notified that the result reports from this run cannot be transferred to GeneRead Link.

Support for new software applications: GeneRead Databank 1.1.0 and QCI Analyze 1.3.0

Improvements

Installed latest security patches for the operation systems.

Unified share concept on the GeneReader Workstation for different scenarios: The technical details of the change will be handled by your QIAGEN field service specialist. However, you may notice during operation of the GeneReader Workstation the new share name "qiagenshare".